| 2024 | AsiaCCS | Switchpoline: A Software Mitigation for Spectre-BTB and Spectre-BHB on ARMv8. | Lorenz Hetterich, Markus Bauer, Michael Schwarz, Christian Rossow |
| 2024 | ICPR | SWJEPA: Improving Prostate Cancer Lesion Detection with Shear Wave Elastography and Joint Embedding Predictive Architectures. | Markus Bauer, Adam Gurwin, Christoph Augenstein, Bogdan Franczyk, Bartosz Malkiewicz |
| 2023 | FedCSIS | Can Unlabelled Data Improve AI Applications? A Comparative Study on Self-Supervised Learning in Computer Vision. | Markus Bauer, Christoph Augenstein |
| 2022 | ACSAC | TyPro: Forward CFI for C-Style Indirect Function Calls Using Type Propagation. | Markus Bauer, Ilya Grishchenko, Christian Rossow |
| 2021 | AsiaCCS | Cali: Compiler-Assisted Library Isolation. | Markus Bauer, Christian Rossow |
| 2010 | WCNC | Enhanced AODV Routing Protocol with Paging in Heterogeneous IP-Based Networks. | Amanpreet Singh, Mariya Goleva, Markus Bauer, Andreas Timm-Giel, Carmelita Grg |
| 2008 | ENTER | A Case Study on Automating Information Aggregation Processes in Information Centres. | Markus Bauer, Christoph Herzog, Hannes Werthner, Birgit Dippelreiter, Kathrin Prantner |
| 2005 | GECCO | Search-based improvement of subsystem decompositions. | Olaf Seng, Markus Bauer, Matthias Biehl, Gert Pache |
| 2005 | WABI | Multiple Structural RNA Alignment with Lagrangian Relaxation. | Markus Bauer, Gunnar W. Klau, Knut Reinert |
| 2004 | ISAAC | Structural Alignment of Two RNA Sequences with Lagrangian Relaxation. | Markus Bauer, Gunnar W. Klau |
| 2003 | GI | Vom Web-Portal zum Web-Desktop. | Tim Romberg, Markus Bauer |
| 1999 | EuroPLop | Support Reengineering by Type Reference - A Reengineering Pattern. | Markus Bauer |